ChIP-seq analysis using R - Experimental design and peak calling.

ChIP-seq analysis using R - Experimental design and peak calling.

Keywords

ChIP-Seq, Experimental-design, Peak-calling, Visualisation

Authors

  • Bori Mifsud
  • Kathi Zarnack

Type

  • Lecture

Description

This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling.

Aims

The aim of the course is to draw biologists' attention to the impact of experimental design, and the pitfalls of ChIP-seq data analysis, and to give them an overview of the analysis steps.

Prerequisites

  • HTS-introduction
  • Preprocessing
  • Alignment

Target audience

  • Biologist
  • Computational biologist

Learning objectives

  • Define appropriate experimental design
  • Describe and perform steps of the ChIP-Seq workflow
  • Explain how peak callers work

Materials

  • not applicable

Data

  • not applicable

Timing

1 hour

Content stability

Stable. There might be small updates in the future.

Technical requirements

  • None

Literature references

  • Landt et al., ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.
  • Chen et al., Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985.

Keywords: ChIP-Seq, Experimental-design, Peak-calling, Visualisation

Authors: Bori Mifsud, Kathi Zarnack

ChIP-seq analysis using R - Experimental design and peak calling. https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-experimental-design-and-peak-calling-cfd4c18f-6c86-45ae-ab0b-630422c76af6 This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling. ChIP-Seq, Experimental-design, Peak-calling, Visualisation